Abstract A number of neurological disorders are characterized by the preferential dysfunction and/or loss of specific neuronal cell populations and the mechanisms underlying this cell type specific vulnerability remain poorly understood. It has been proposed that the differential neuronal vulnerability observed in these disorders arises from disruptions in cell type specific gene expression regulatory programs responsible for maintaining the physiological identity and function of the affected neurons. MicroRNAs (miRNAs) are small, non-coding RNAs involved in the regulation of gene expression networks at the posttranscriptional level. Studies, including ours, have implicated altered miRNA expression in the pathogenicity of several neurological disorders. Here, we propose the development of a novel molecular approach to investigate the role that neural cell type specific changes in miRNA function play in the pathogenicity of neurological diseases. The approach relies on a recombinant adeno-associated virus (rAAV)-based, Cre recombinase-dependent genetic Flp-excision switch (FLEX switch) that restricts the expression of an ectopically delivered miRNA-binding protein Argonaute-2 to Cre expressing cells. We call this approach miFLAGO (miRNA-associated, FLEX switch regulated, AGO2). Experiments in Aim-1 will validate the functionality and reproducibility of miFLEX in the cerebellum of adult transgenic mice engineered to selectively express Cre recombinase in Purkinje cells. Purkinje cell-specific miFAGO-miRNA complexes will be isolated and used to build miRNA libraries for high-throughput RNA sequencing analysis. In Aim-2, we will use miFLAGO to investigate the role that cell type specific changes in miRNA function play in the pathogenicity of a mouse model of Spinocerebellar ataxia type-1, a polyglutamine disorder caused by the expansion of a CAG repeat in the ATXN1 gene. The short-term goal of this proposal is to provide the research community with a validated novel molecular tool for the study of cell type specific miRNA function. Long-term, we aim to fine-tune our understanding of neural cell type specific gene expression regulatory programs and how they might mediate differential vulnerability in neurological disease, with the goal of identifying novel therapeutic routes.